RNA-Seq mapping and detection of gene fusions with a suffix array algorithm

Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian GuKelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui

Research output: Contribution to journalArticle

32 Scopus citations


High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions-particularly those expressed with low abundance- is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample.

Original languageEnglish (US)
Article numbere1002464
JournalPLoS computational biology
Issue number4
StatePublished - Apr 2012

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

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    Sakarya, O., Breu, H., Radovich, M., Chen, Y., Wang, Y. N., Barbacioru, C., Utiramerur, S., Whitley, P. P., Brockman, J. P., Vatta, P., Zhang, Z., Popescu, L., Muller, M. W., Kudlingar, V., Garg, N., Li, C. Y., Kong, B. S., Bodeau, J. P., Nutter, R. C., ... Siddiqui, A. S. (2012). RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS computational biology, 8(4), [e1002464]. https://doi.org/10.1371/journal.pcbi.1002464